Chilli
High Treason Prevention Officer
Certainly Moffat will want to do things his own way and take the show in his own direction, but, we can hope that he and RTD sat down and discussed where Moff wanted to start from. For example, Moff might have said "I want to start with a Black Guardian/White Guardian story arc, can you slip in a mystery person (I think I want to use a woman for the White Guardian this time) for me to pick up the thread with". Or, he might have said he wants be able to play with the Time Lords, so, he might have suggested RTD open that door up for him to expand upon, etc.
Or maybe not....
It's possible, but Moff and RTD don't have a good track record here.
A lot of people were bugged, back in season 2, about "The Girl in the Fireplace" not fitting in with the rest of the season. While that season had this big Rose-Doctor-Love thing going on, The Girl in the Fireplace had the doctor chasing after some French broad, and Rose not really caring either way about this.
Apparently this happened because ... RTD didn't inform Moff about his plans for the season, and Moff didn't care to ask about his plans. So he simply didn't know that Rose was supposed to have the hots for the Doctor.
I suspect Moff won't contradict any of the continuity established by RTD, but I'd be surprised if he went out of his way to tie up any of his loose ends. We shall see.